comparison fastq-join.xml @ 4:de9bb59a9923 draft default tip

planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastq_join commit a7f8461032de196092033c9ceae9f4407a469c44

3:c8ed841ebe78

<tool id="fastq_join" name="fastq-join" version="1.1.2-806">
    <description> - Joins two paired-end reads on the overlapping ends</description>

    <requirements>
        <requirement type="package" version="1.1.2-806">ea-utils</requirement>
    </requirements>

        <exit_code range="1:" level="fatal" description="Unknown error occurred" />
    </stdio>

    <command><![CDATA[
        fastq-join
        -v '$splitChar'
        -p $pctMaxDiff
        -m $minOverlap
        #if $stitchLengthReport:
        -r $outputStitchLengthReport
        #end if
        $read1
        $read2
        -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined
        ]]>
    </command>

    <inputs>
        <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" />
        <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" />
        <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" />
        <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" />
        <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" />
        <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" />
    </inputs>

    <outputs>
        <data format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
        <data format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
        <data format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
        <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)">
            <filter>stitchLengthReport</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="read1" value="test_read1.fastq" />
            <param name="read2" value="test_read3.fastq" />
            <output name="outputJoined" file="testout.join.fastq" />
            <output name="outputUnmatched1" file="testout.un1.fastq" />
            <output name="outputUnmatched2" file="testout.un2.fastq" />
        </test>
    </tests>

4:de9bb59a9923

<tool id="fastq_join" name="fastq-join" version="1.1.2-806.1">
    <description> - Joins two paired-end reads on the overlapping ends</description>

    <requirements>
        <requirement type="package" version="1.1.2-806">ea-utils</requirement>
    </requirements>

        <exit_code range="1:" level="fatal" description="Unknown error occurred" />
    </stdio>

    <command><![CDATA[
        fastq-join
        -v "${splitChar}"
        -p "${pctMaxDiff}"
        -m "${minOverlap}"
        #if $stitchLengthReport:
        -r "${outputStitchLengthReport}"
        #end if
        #if str( $input_type.input_type_selector ) == 'paired':
            "${input_type.read1}"
            "${input_type.read2}"
        #else:
            "${input_type.input_collection.forward}"
            "${input_type.input_collection.reverse}"
        #end if
        -o "${outputUnmatched1}" -o "${outputUnmatched2}" -o "${outputJoined}"
        ]]>
    </command>

    <inputs>
      <conditional name="input_type">
            <param name="input_type_selector" type="select" label="Dataset type">
              <option value="paired">Paired-end</option>
              <option value="paired_collection">Paired-end Dataset Collection</option>
            </param>
            <when value="paired">
                <param format="fastqsanger" name="read1" type="data" label="Read 1 Fastq" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." />
                <param format="fastqsanger" name="read2" type="data" label="Read 2 Fastq" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." />
            </when>
            <when value="paired_collection">
                <param name="input_collection" format="fastqsanger"
                    type="data_collection" collection_type="paired"
                    label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." />
            </when>
        </conditional>
        <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" />
        <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" />
        <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" />
        <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" />
    </inputs>

    <outputs>
        <data format="fastqsanger" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
        <data format="fastqsanger" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
        <data format="fastqsanger" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
        <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)">
            <filter>stitchLengthReport</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="read1" value="test_read1.fastq" ftype="fastqsanger" />
            <param name="read2" value="test_read3.fastq" ftype="fastqsanger" />
            <output name="outputJoined" file="testout.join.fastq" />
            <output name="outputUnmatched1" file="testout.un1.fastq" />
            <output name="outputUnmatched2" file="testout.un2.fastq" />
        </test>
    </tests>